Friday, December 20, 2013

Mass spec free proteomics!?!?!

Lets start off like this:  This is a paper in MCP but they didnt do any mass spectrometry, not even a little, so why do we care?

Next article please!

No, wait!  This is awesome, I promise.

You know how I'm always preaching that the database ought to match the size of the thing we're doing MS/MS on?  Why on earth would we go to all the work of cutting a liver out of something, doing proteomics on it, and then searching all of the proteins that mice can produce?  Does that make sense?  Nope!  But there isn't much we can do about it.

But what if somebody took the genome and cut it down to what proteins are expressed in what tissues by doing RNASeq on individual tissues?

And what if they backed it up with protein arrays to show that the protein levels strongly correlate with the transript levels?

In my (humble?) opinion, thats a paper that ought to be in MCP!

Who needs a mass spec?  Wait! What?  Everybody!  But this is pretty cool and will be helpful later!!  Lets try re-running that brain, liver, or whatever with a FASTA that only contains proteins from that organ and see how our results jump through the roof and our FDR drops through the floor!

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